From what I gather the change was actually made a while ago, which allowed the researchers at Cellzome to use older sets of 6-Plex (before the change) and newer sets of 6-Plex (after the change) to make their own 8-Plex (this was the paper that came out separate of Proteome Sciences).

The documentation for the new six-plex product can be found here, and you can see in the structures that ETD produces reporter ions for all six tags that are currently being sold. I hope this helps and if you have any more questions feel free to ask.

Correct. It is something that was not made widely known. I did not even realize it until the 8-Plex paper from Cellzome came out and explained why the change was made. However, with the change it is now straight forward to do quantitation with ETD. However, no one in our lab has tried this.

Two of the first papers I published were on this exact topic. Here are the links (paper #1and paper #2) but I can summarize them for you here.

Technically, yes they do work but have less channels (4-plex becomes 3-plex, 8-plex becomes 5-plex). If you do ms3 on a common fragment ion you can get the full 4 or 8 plexes back. But the really problem is that ETD does not routinely give rise to abundant reporter ions so the quantitation is not always great. I believe newer versions of TMT have been modified so that you can get all 6 channels of quant without doing MS3 but I haven't tried them. In general though, beam-type CAD is a better choice for quantitation. If you really need ETD for fragmentation I would recommend doing 2 MS-scans for every precursor (1 beam-type CAD and 1 ETD).